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Re: [OWLAPI-developer] How to get the annotation of an OWLAxiom, particularly Equivalent Class
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From: An C. T. <tca...@gm...> - 2011-06-28 13:23:04
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Bravo, Ignazio!
I don't know whether this is a bug or not but your idea works well.
Thanks so much.
An.
On 28/06/11 6:38 PM, Ignazio Palmisano wrote:
> 2011/6/28 An C. Tran<tca...@gm...>:
>> Thank you so much for your kind help, Ignazio.
>>
>> I executed your code with both OWLAPI v3.2.3 and the one that is shipped
>> with Pellet 2.2.2 and both them worked well. So, the problem should be a
>> bug in Pellet that prevent returning the annotation of axioms? Do you
>> have any idea about this problem?
> I wouldn't call it a bug. I believe the axioms you're obtaining in the
> explanation are not the very same objects that are in the ontology but
> are created on demand for the explanation (some explanation techniques
> can break the axioms into parts to make the explanation laconic), so
> they would not carry the annotations of the original axiom. It might
> happen that the axiom being used in the explanation is the same as the
> original axiom in the ontology, in which case the annotations appear
> to be lost.
>
>> If we cannot fix that bug in Pellet, I
>> think we can get a solution with the help of OWLAPI. Do you think so?
> You can try one simple workaround:
>
> - iterate over all axioms in the ontology
> - for each axiom A, call the getAxiomWithoutAnnotations() and put that
> into B - this will give you the axiom with annotations removed
> - in a map, put B -> A
>
> Then, take the axioms from the explanation and check whether the map
> contains them as keys; those which are in the map correspond to
> annotated axioms, and you can get the annotations from the value
> corresponding to that key (axiom equals() method is supposed to take
> into account the annotations).
>
> HTH,
> I.
>
>
>> Thank you.
>> An.
>>
>>
>> On 6/27/2011 9:06 PM, Ignazio Palmisano wrote:
>>> 2011/6/27 An C. Tran<tca...@gm...>:
>>>> Hi all,
>>>>
>>>> Someone can help me with this:
>>>>
>>>> In my example, given an "OWLAxiom eq" is an EquivalentClass, the following
>>>> segment of code:
>>>> System.out.println("\n***" + eq.getAxiomType() + ":");
>>>> System.out.println("Annotation: " + eq.getAnnotations());
>>>> System.out.println(renderer.render(eq));
>>>>
>>> Hi,
>>> I tried your code (with some changes to remove calls to Pellet) with
>>> the latest OWL API and I get this output:
>>>
>>> Reading file file:///Users/ignazio/Downloads/abd.muse.massey.ac.nz.owl...Ontology
>>> loaded
>>>
>>> ***EquivalentClasses:
>>> Annotation: [Annotation(rdfs:label "DurationAbnormality_Showering"^^xsd:string)]
>>> DurationAbnormality EquivalentTo Showering and (activityHasDuration some
>>> (Duration and ((hasDurationValue some double[> 15]) or
>>> (hasDurationValue some double[< 5])))) and (activityHasStarttime some
>>> Winter)
>>>
>>> ***EquivalentClasses:
>>> Annotation: [Annotation(rdfs:label "DurationAbnormality_Toileting"^^xsd:string)]
>>> DurationAbnormality EquivalentTo Toileting and (activityHasDuration some
>>> (Duration and (hasDurationValue some double[> 15])))
>>>
>>> ***EquivalentClasses:
>>> Annotation: [Annotation(rdfs:label "EquivalentWinter_Ann")]
>>> Winter EquivalentTo Timepoint and (hasMonthValue some double[>= 5])
>>> and (hasMonthValue some double[<= 8])
>>>
>>>
>>> for this code:
>>>
>>> public class Explanation_EquiClass_Lite {
>>> private static final String file =
>>> "file:///Users/ignazio/Downloads/abd.muse.massey.ac.nz.owl";
>>> private static OWLObjectRenderer renderer = new
>>> ManchesterOWLSyntaxOWLObjectRendererImpl(); //new
>>> DLSyntaxObjectRenderer();
>>>
>>> public static void main(String[] args) throws Exception {
>>> System.out.print("Reading file " + file + "...");
>>> OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
>>> OWLOntology ontology = manager.loadOntology(IRI.create(file));
>>> OWLDataFactory factory = manager.getOWLDataFactory();
>>> System.out.println("Ontology loaded");
>>> OWLAnnotationProperty label = factory.getRDFSLabel();
>>> for (OWLAxiom e : ontology.getAxioms()) {
>>> Set<OWLAnnotation> labels = e.getAnnotations(label);
>>> if (labels.size()> 0) {
>>> System.out.println("\n***" + e.getAxiomType() + ":");
>>> System.out.println("Annotation: " + labels);
>>> System.out.println(renderer.render(e));
>>> }
>>> }
>>> }
>>> }
>>>
>>>
>>> I assume you're using Pellet 2.2.2 and the OWL API which ships with
>>> it, which is from March 2010 IIRC. There might be bugs in that version
>>> of the OWL API, or Pellet might be returning the axioms stripped of
>>> the annotations. You can try Pellet with the latest release (3.2.3),
>>> if the bug is in the OWL API that should fix it.
>>> HTH,
>>> I.
>>>
>>>> produces the following result:
>>>> ***EquivalentClasses:
>>>> Annotation: []
>>>> DurationAbnormality EquivalentTo Showering and ......
>>>>
>>>> The annotation is always empty while I assigned annotation for this
>>>> EquivalentClass before.
>>>> However, it runs well for classes.
>>>>
>>>> I attached my ontology and java code for your checking.
>>>>
>>>>
>>>> Cheers,
>>>> An.
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> All of the data generated in your IT infrastructure is seriously valuable.
>>>> Why? It contains a definitive record of application performance, security
>>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>>> sense of it. IT sense. And common sense.
>>>> http://p.sf.net/sfu/splunk-d2d-c2
>>>> _______________________________________________
>>>> Owlapi-developer mailing list
>>>> Owl...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/owlapi-developer
>>>>
>>>>
>>> ------------------------------------------------------------------------------
>>> All of the data generated in your IT infrastructure is seriously valuable.
>>> Why? It contains a definitive record of application performance, security
>>> threats, fraudulent activity, and more. Splunk takes this data and makes
>>> sense of it. IT sense. And common sense.
>>> http://p.sf.net/sfu/splunk-d2d-c2
>>> _______________________________________________
>>> Owlapi-developer mailing list
>>> Owl...@li...
>>> https://lists.sourceforge.net/lists/listinfo/owlapi-developer
>>
>> ------------------------------------------------------------------------------
>> All of the data generated in your IT infrastructure is seriously valuable.
>> Why? It contains a definitive record of application performance, security
>> threats, fraudulent activity, and more. Splunk takes this data and makes
>> sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-d2d-c2
>> _______________________________________________
>> Owlapi-developer mailing list
>> Owl...@li...
>> https://lists.sourceforge.net/lists/listinfo/owlapi-developer
>>
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> _______________________________________________
> Owlapi-developer mailing list
> Owl...@li...
> https://lists.sourceforge.net/lists/listinfo/owlapi-developer
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